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<div class="section" id="domaindecomposition-objects">
<h1>DomainDecomposition objects<a class="headerlink" href="#domaindecomposition-objects" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="quippy.atoms.DomainDecomposition">
<em class="property">class </em><code class="descclassname">quippy.atoms.</code><code class="descname">DomainDecomposition</code><span class="sig-paren">(</span><span class="optional">[</span><em>decomposition</em>, <em>verlet_shell</em>, <em>mode</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType" title="quippy.oo_fortran.FortranDerivedType"><code class="xref py py-class docutils literal notranslate"><span class="pre">quippy.oo_fortran.FortranDerivedType</span></code></a></p>
<p>Initialize the domain decomposition module</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>decomposition</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (3), optional</span></dt>
<dd></dd>
<dt><strong>verlet_shell</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input float, optional</span></dt>
<dd></dd>
<dt><strong>mode</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int, optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">__init__initialise</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.
Class is wrapper around Fortran type <code class="docutils literal notranslate"><span class="pre">DomainDecomposition</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Attributes:</th><td class="field-body"><dl class="first last docutils">
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.atoms_properties" title="quippy.atoms.DomainDecomposition.atoms_properties"><code class="xref py py-obj docutils literal notranslate"><span class="pre">atoms_properties</span></code></a></dt>
<dd><p class="first last">Fields to communicate if for particles</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.center" title="quippy.atoms.DomainDecomposition.center"><code class="xref py py-obj docutils literal notranslate"><span class="pre">center</span></code></a></dt>
<dd><p class="first last">Center of the domain</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.decomposed" title="quippy.atoms.DomainDecomposition.decomposed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">decomposed</span></code></a></dt>
<dd><p class="first last">True if domain decomposition is active</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.decomposition" title="quippy.atoms.DomainDecomposition.decomposition"><code class="xref py py-obj docutils literal notranslate"><span class="pre">decomposition</span></code></a></dt>
<dd><p class="first last">Type of decomposition</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.ghost_properties" title="quippy.atoms.DomainDecomposition.ghost_properties"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ghost_properties</span></code></a></dt>
<dd><p class="first last">Fields to communicate for ghosts</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.ghosts_l" title="quippy.atoms.DomainDecomposition.ghosts_l"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ghosts_l</span></code></a></dt>
<dd><p class="first last">particles send to the left (where they become ghosts)</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.ghosts_r" title="quippy.atoms.DomainDecomposition.ghosts_r"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ghosts_r</span></code></a></dt>
<dd><p class="first last">particles send to the right (where they become ghosts)</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.global_to_local" title="quippy.atoms.DomainDecomposition.global_to_local"><code class="xref py py-obj docutils literal notranslate"><span class="pre">global_to_local</span></code></a></dt>
<dd><p class="first last">Global index to local index</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.l" title="quippy.atoms.DomainDecomposition.l"><code class="xref py py-obj docutils literal notranslate"><span class="pre">l</span></code></a></dt>
<dd><p class="first last">Ranks of left domains in x-, y- and z-direction</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.lower" title="quippy.atoms.DomainDecomposition.lower"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lower</span></code></a></dt>
<dd><p class="first last">Lower domain boundary, in fraction of the total cell</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.lower_with_border" title="quippy.atoms.DomainDecomposition.lower_with_border"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lower_with_border</span></code></a></dt>
<dd><p class="first last">Lower domain boundary, including border</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.mpi" title="quippy.atoms.DomainDecomposition.mpi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mpi</span></code></a></dt>
<dd><p class="first last">MPI communicator</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.n_ghosts_l" title="quippy.atoms.DomainDecomposition.n_ghosts_l"><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_ghosts_l</span></code></a></dt>
<dd><p class="first last">length of the ghost particle lists (left)</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.n_ghosts_r" title="quippy.atoms.DomainDecomposition.n_ghosts_r"><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_ghosts_r</span></code></a></dt>
<dd><p class="first last">length of the ghost particle lists (right)</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.n_recv_g_tot" title="quippy.atoms.DomainDecomposition.n_recv_g_tot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_recv_g_tot</span></code></a></dt>
<dd><p class="first last">Statistics: Number of total ghosts received</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.n_recv_p_tot" title="quippy.atoms.DomainDecomposition.n_recv_p_tot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_recv_p_tot</span></code></a></dt>
<dd><p class="first last">Statistics: Number of total particles received</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.n_send_g_tot" title="quippy.atoms.DomainDecomposition.n_send_g_tot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_send_g_tot</span></code></a></dt>
<dd><p class="first last">Statistics: Number of total ghosts send</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.n_send_p_tot" title="quippy.atoms.DomainDecomposition.n_send_p_tot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_send_p_tot</span></code></a></dt>
<dd><p class="first last">Statistics: Number of total particles send</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.nit_g" title="quippy.atoms.DomainDecomposition.nit_g"><code class="xref py py-obj docutils literal notranslate"><span class="pre">nit_g</span></code></a></dt>
<dd><p class="first last">Statistics: Number of ghost send events</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.nit_p" title="quippy.atoms.DomainDecomposition.nit_p"><code class="xref py py-obj docutils literal notranslate"><span class="pre">nit_p</span></code></a></dt>
<dd><p class="first last">Statistics: Number of particle send events</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.ntotal" title="quippy.atoms.DomainDecomposition.ntotal"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ntotal</span></code></a></dt>
<dd><p class="first last">Number of total particles in this simulation</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.off_l" title="quippy.atoms.DomainDecomposition.off_l"><code class="xref py py-obj docutils literal notranslate"><span class="pre">off_l</span></code></a></dt>
<dd><p class="first last">Distance vector to left domain</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.off_r" title="quippy.atoms.DomainDecomposition.off_r"><code class="xref py py-obj docutils literal notranslate"><span class="pre">off_r</span></code></a></dt>
<dd><p class="first last">Distance vector to right domain</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.periodic" title="quippy.atoms.DomainDecomposition.periodic"><code class="xref py py-obj docutils literal notranslate"><span class="pre">periodic</span></code></a></dt>
<dd><p class="first last">Periodicity for domain decomposition</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.r" title="quippy.atoms.DomainDecomposition.r"><code class="xref py py-obj docutils literal notranslate"><span class="pre">r</span></code></a></dt>
<dd><p class="first last">Ranks of right domains in x-, y- and z-direction</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.recv_l" title="quippy.atoms.DomainDecomposition.recv_l"><code class="xref py py-obj docutils literal notranslate"><span class="pre">recv_l</span></code></a></dt>
<dd><p class="first last">buffer for receiving from the left</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.recv_r" title="quippy.atoms.DomainDecomposition.recv_r"><code class="xref py py-obj docutils literal notranslate"><span class="pre">recv_r</span></code></a></dt>
<dd><p class="first last">buffer for receiving from the right</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.reverse_properties" title="quippy.atoms.DomainDecomposition.reverse_properties"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reverse_properties</span></code></a></dt>
<dd><p class="first last">Back-communication after force computations</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.send_l" title="quippy.atoms.DomainDecomposition.send_l"><code class="xref py py-obj docutils literal notranslate"><span class="pre">send_l</span></code></a></dt>
<dd><p class="first last">buffer for sending to the left</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.send_r" title="quippy.atoms.DomainDecomposition.send_r"><code class="xref py py-obj docutils literal notranslate"><span class="pre">send_r</span></code></a></dt>
<dd><p class="first last">buffer for sending to the right</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.upper" title="quippy.atoms.DomainDecomposition.upper"><code class="xref py py-obj docutils literal notranslate"><span class="pre">upper</span></code></a></dt>
<dd><p class="first last">Upper domain boundary, in fraction of the total cell</p>
</dd>
<dt><a class="reference internal" href="#quippy.atoms.DomainDecomposition.upper_with_border" title="quippy.atoms.DomainDecomposition.upper_with_border"><code class="xref py py-obj docutils literal notranslate"><span class="pre">upper_with_border</span></code></a></dt>
<dd><p class="first last">Upper domain boundary, including border</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">Methods</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.allocate" title="quippy.atoms.DomainDecomposition.allocate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">allocate</span></code></a>(at,[range,error])</td>
<td>Assign global indices Allocate internal buffer</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.comm_atoms" title="quippy.atoms.DomainDecomposition.comm_atoms"><code class="xref py py-obj docutils literal notranslate"><span class="pre">comm_atoms</span></code></a>(at,[error])</td>
<td>Communicate particles which left the domains to the neighboring domains (former order routine)</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.comm_atoms_to_all" title="quippy.atoms.DomainDecomposition.comm_atoms_to_all"><code class="xref py py-obj docutils literal notranslate"><span class="pre">comm_atoms_to_all</span></code></a>(at,[error])</td>
<td>Communicate all particles from this domain to all other domains</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.comm_ghosts" title="quippy.atoms.DomainDecomposition.comm_ghosts"><code class="xref py py-obj docutils literal notranslate"><span class="pre">comm_ghosts</span></code></a>(at,new_list,[error])</td>
<td>Communicate ghost particles to neighboring domains (former prebinning routine).</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.comm_reverse" title="quippy.atoms.DomainDecomposition.comm_reverse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">comm_reverse</span></code></a>(at,[error])</td>
<td>Communicate forces of ghost particles back.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.deepcopy" title="quippy.atoms.DomainDecomposition.deepcopy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">deepcopy</span></code></a>(from)</td>
<td>Create a deep copy</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.disable" title="quippy.atoms.DomainDecomposition.disable"><code class="xref py py-obj docutils literal notranslate"><span class="pre">disable</span></code></a>(at,[error])</td>
<td>Disable domain decomposition, after this call every process retains an identical copy of the system.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.enable" title="quippy.atoms.DomainDecomposition.enable"><code class="xref py py-obj docutils literal notranslate"><span class="pre">enable</span></code></a>(…)</td>
<td>Enable domain decomposition, after this call every process remains only with the atoms in its local domain.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.set_border" title="quippy.atoms.DomainDecomposition.set_border"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_border</span></code></a>(at,border,[verlet_shell,error])</td>
<td>Set the communication border</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.atoms.DomainDecomposition.set_comm_property" title="quippy.atoms.DomainDecomposition.set_comm_property"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_comm_property</span></code></a>(…)</td>
<td>Set which properties to communicate on which events comm_atoms:   Communicate when atom is moved to different domain.</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.allocate">
<code class="descname">allocate</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>range</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.allocate" title="Permalink to this definition">¶</a></dt>
<dd><p>Assign global indices
Allocate internal buffer</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>range</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (2), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">__init__allocate</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.comm_atoms">
<code class="descname">comm_atoms</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.comm_atoms" title="Permalink to this definition">¶</a></dt>
<dd><p>Communicate particles which left the domains
to the neighboring domains (former order routine)</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">comm_atoms</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.comm_atoms_to_all">
<code class="descname">comm_atoms_to_all</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.comm_atoms_to_all" title="Permalink to this definition">¶</a></dt>
<dd><p>Communicate all particles from this domain to all other domains</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">comm_atoms_to_all</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.comm_ghosts">
<code class="descname">comm_ghosts</code><span class="sig-paren">(</span><em>at</em>, <em>new_list</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.comm_ghosts" title="Permalink to this definition">¶</a></dt>
<dd><p>Communicate ghost particles to neighboring domains
(former prebinning routine). <em>bwidth</em> is the width of
the border.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>new_list</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">comm_ghosts</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.comm_reverse">
<code class="descname">comm_reverse</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.comm_reverse" title="Permalink to this definition">¶</a></dt>
<dd><p>Communicate forces of ghost particles back.
This is needed for rigid object (i.e., water) or to reduce the
border size in BOPs.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">comm_reverse</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.deepcopy">
<code class="descname">deepcopy</code><span class="sig-paren">(</span><em>from</em><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.deepcopy" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a deep copy</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
<dt><strong>from</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="#quippy.atoms.DomainDecomposition" title="quippy.atoms.DomainDecomposition"><code class="xref py py-class docutils literal notranslate"><span class="pre">DomainDecomposition</span></code></a> object</span></dt>
<dd></dd>
</dl>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>to</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="#quippy.atoms.DomainDecomposition" title="quippy.atoms.DomainDecomposition"><code class="xref py py-class docutils literal notranslate"><span class="pre">DomainDecomposition</span></code></a> object</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">deepcopy</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.disable">
<code class="descname">disable</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.disable" title="Permalink to this definition">¶</a></dt>
<dd><p>Disable domain decomposition, after this call every process
retains an identical copy of the system.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">disable</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.enable">
<code class="descname">enable</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mpi</em>, <em>decomposition</em>, <em>verlet_shell</em>, <em>mode</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.enable" title="Permalink to this definition">¶</a></dt>
<dd><p>Enable domain decomposition, after this call every process
remains only with the atoms in its local domain.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>mpi</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="mpi_context.html#quippy.mpi_context.MPI_context" title="quippy.mpi_context.MPI_context"><code class="xref py py-class docutils literal notranslate"><span class="pre">MPI_context</span></code></a> object, optional</span></dt>
<dd></dd>
<dt><strong>decomposition</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (3), optional</span></dt>
<dd></dd>
<dt><strong>verlet_shell</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input float, optional</span></dt>
<dd></dd>
<dt><strong>mode</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int, optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">enable</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.set_border">
<code class="descname">set_border</code><span class="sig-paren">(</span><em>at</em>, <em>border</em><span class="optional">[</span>, <em>verlet_shell</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.set_border" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the communication border</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>border</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input float</span></dt>
<dd></dd>
<dt><strong>verlet_shell</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input float, optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">set_border</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.atoms.DomainDecomposition.set_comm_property">
<code class="descname">set_comm_property</code><span class="sig-paren">(</span><em>propname</em><span class="optional">[</span>, <em>comm_atoms</em>, <em>comm_ghosts</em>, <em>comm_reverse</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.atoms.DomainDecomposition.set_comm_property" title="Permalink to this definition">¶</a></dt>
<dd><p>Set which properties to communicate on which events
comm_atoms:   Communicate when atom is moved to different domain.</p>
<blockquote>
<div>Forces, for example, may be excluded since they are updated
on every time step.</div></blockquote>
<dl class="docutils">
<dt>comm_ghosts:  Communicate when atoms becomes a ghost on some domain</dt>
<dd>Masses, for example, might be excluded since atoms are
propagated on the domain they reside in only.</dd>
<dt>comm_reverse: Communicate back from ghost atoms to the original domain atom</dt>
<dd>and accumulate</dd>
</dl>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>propname</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input string(len=-1)</span></dt>
<dd></dd>
<dt><strong>comm_atoms</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int, optional</span></dt>
<dd></dd>
<dt><strong>comm_ghosts</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int, optional</span></dt>
<dd></dd>
<dt><strong>comm_reverse</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int, optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">set_comm_property</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/Atoms_types.f95">src/libAtoms/Atoms_types.f95</a>.</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.atoms_properties">
<code class="descname">atoms_properties</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.atoms_properties" title="Permalink to this definition">¶</a></dt>
<dd><p>Fields to communicate if for particles</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.center">
<code class="descname">center</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.center" title="Permalink to this definition">¶</a></dt>
<dd><p>Center of the domain</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.decomposed">
<code class="descname">decomposed</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.decomposed" title="Permalink to this definition">¶</a></dt>
<dd><p>True if domain decomposition is active</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.decomposition">
<code class="descname">decomposition</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.decomposition" title="Permalink to this definition">¶</a></dt>
<dd><p>Type of decomposition</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.ghost_properties">
<code class="descname">ghost_properties</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.ghost_properties" title="Permalink to this definition">¶</a></dt>
<dd><p>Fields to communicate for ghosts</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.ghosts_l">
<code class="descname">ghosts_l</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.ghosts_l" title="Permalink to this definition">¶</a></dt>
<dd><p>particles send to the left (where they become ghosts)</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.ghosts_r">
<code class="descname">ghosts_r</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.ghosts_r" title="Permalink to this definition">¶</a></dt>
<dd><p>particles send to the right (where they become ghosts)</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.global_to_local">
<code class="descname">global_to_local</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.global_to_local" title="Permalink to this definition">¶</a></dt>
<dd><p>Global index to local index</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.l">
<code class="descname">l</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.l" title="Permalink to this definition">¶</a></dt>
<dd><p>Ranks of left domains in x-, y- and z-direction</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.lower">
<code class="descname">lower</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.lower" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower domain boundary, in fraction of the total cell</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.lower_with_border">
<code class="descname">lower_with_border</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.lower_with_border" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower domain boundary, including border</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.mpi">
<code class="descname">mpi</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.mpi" title="Permalink to this definition">¶</a></dt>
<dd><p>MPI communicator</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.n_ghosts_l">
<code class="descname">n_ghosts_l</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.n_ghosts_l" title="Permalink to this definition">¶</a></dt>
<dd><p>length of the ghost particle lists (left)</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.n_ghosts_r">
<code class="descname">n_ghosts_r</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.n_ghosts_r" title="Permalink to this definition">¶</a></dt>
<dd><p>length of the ghost particle lists (right)</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.n_recv_g_tot">
<code class="descname">n_recv_g_tot</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.n_recv_g_tot" title="Permalink to this definition">¶</a></dt>
<dd><p>Statistics: Number of total ghosts received</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.n_recv_p_tot">
<code class="descname">n_recv_p_tot</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.n_recv_p_tot" title="Permalink to this definition">¶</a></dt>
<dd><p>Statistics: Number of total particles received</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.n_send_g_tot">
<code class="descname">n_send_g_tot</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.n_send_g_tot" title="Permalink to this definition">¶</a></dt>
<dd><p>Statistics: Number of total ghosts send</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.n_send_p_tot">
<code class="descname">n_send_p_tot</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.n_send_p_tot" title="Permalink to this definition">¶</a></dt>
<dd><p>Statistics: Number of total particles send</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.nit_g">
<code class="descname">nit_g</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.nit_g" title="Permalink to this definition">¶</a></dt>
<dd><p>Statistics: Number of ghost send events</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.nit_p">
<code class="descname">nit_p</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.nit_p" title="Permalink to this definition">¶</a></dt>
<dd><p>Statistics: Number of particle send events</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.ntotal">
<code class="descname">ntotal</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.ntotal" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of total particles in this simulation</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.off_l">
<code class="descname">off_l</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.off_l" title="Permalink to this definition">¶</a></dt>
<dd><p>Distance vector to left domain</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.off_r">
<code class="descname">off_r</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.off_r" title="Permalink to this definition">¶</a></dt>
<dd><p>Distance vector to right domain</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.periodic">
<code class="descname">periodic</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.periodic" title="Permalink to this definition">¶</a></dt>
<dd><p>Periodicity for domain decomposition</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.r">
<code class="descname">r</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.r" title="Permalink to this definition">¶</a></dt>
<dd><p>Ranks of right domains in x-, y- and z-direction</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.recv_l">
<code class="descname">recv_l</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.recv_l" title="Permalink to this definition">¶</a></dt>
<dd><p>buffer for receiving from the left</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.recv_r">
<code class="descname">recv_r</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.recv_r" title="Permalink to this definition">¶</a></dt>
<dd><p>buffer for receiving from the right</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.reverse_properties">
<code class="descname">reverse_properties</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.reverse_properties" title="Permalink to this definition">¶</a></dt>
<dd><p>Back-communication after force computations</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.send_l">
<code class="descname">send_l</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.send_l" title="Permalink to this definition">¶</a></dt>
<dd><p>buffer for sending to the left</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.send_r">
<code class="descname">send_r</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.send_r" title="Permalink to this definition">¶</a></dt>
<dd><p>buffer for sending to the right</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.upper">
<code class="descname">upper</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.upper" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper domain boundary, in fraction of the total cell</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.atoms.DomainDecomposition.upper_with_border">
<code class="descname">upper_with_border</code><a class="headerlink" href="#quippy.atoms.DomainDecomposition.upper_with_border" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper domain boundary, including border</p>
</dd></dl>

</dd></dl>

</div>


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